The mbc3.m script that comes with the MBC3 toolset can only be used if you have a system with some states in the rotating frame. If you want to analyze a system with all states in the fixed frame, you can use the cce.m script supplied with the MBC3 toolset. The cce.m script performs the eigenanalysis directly on the azimuth-averaged state matrix, AvgAMat (regardless of whether or not the system has states in the rotating frame). This is perfectly suitable for a system with only states in the fixed frame. (For a system with some states in the rotating frame, the cce.m script employs the constant-coefficient-approximation eigenanalysis.)